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Such a stupid question, the Pokémon Mansion, like everything else except the Pokémon Center (for whatever reason) got destroyed by the volcano. Why should it matter that it's now missing after three years in between games? It wasn't like people were still using it, it was just full of wild Pokémon and lost items that burglars would occasionally find. Far as I know, only a few people have found and read the diaries, not including the player. Obviously, the scientist(s) didn't care much for the diary entries. How else would it explain them being left there?

Now, if you want an out-of-universe explanation, it's because there's only so much you can put in a GameBoy cartridge. Considering that they had to program the whole main story before, Kanto being just a post-credits bonus, GameFreak didn't have space enough left to program all of Kanto into the games; so they "abridged" it in some parts and removed some other places, coming up with some in-universe excuses for their absence. That's why Viridian Forest was cut down, Cinnabar was destroyed, Cerulean Cave was blocked, Pokémon Tower became Radio Tower and you can't go past the first floor — they simply didn't have enough space left in the cartridge for the entirety of Kanto.

Everything except the Pokémon Center in Cinnabar Island got destroyed by the volcanoare you living under a rock?

I'll guess that the original pokecentre was actually destroyed along with all other buildings in Cinnabar Island, however the Pokecentre was rebuilt, because it was important for the lives of nearby pokemon and trainer's pokemon nearby.

Though Ver-Mont is spot on with what the actual reason is.

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The above posters hit the nail on the head, especially Ver-mont. If you're wondering why anything else in Kanto is missing, you can bet it's because there just wasn't room for it. Since the question has been answered, I'm closing this.